Contacts of the helix formed by residues 263 - 280 (chain A) in PDB entry 4XH9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 4.6 1.6 - - + +
193A LEU* 4.0 12.8 - - - +
221A ASP 5.1 0.2 - - - -
222A LEU 4.1 10.3 + - - -
225A TYR* 3.7 33.7 - + + +
228A LEU* 4.6 2.5 - - + -
229A HIS* 2.5 43.9 + + - -
260A LEU* 3.1 30.1 + - + +
261A ASN 3.0 2.0 + - - -
262A ALA* 1.3 76.5 - - + +
264A ARG* 1.3 63.7 + - - +
265A GLY 3.3 1.8 - - - -
266A TYR* 3.3 12.3 + - + +
267A CYS* 3.0 27.7 + - - +
311A PRO* 3.7 35.2 - - + -
315A LEU* 3.9 26.2 - - + -
353A ILE* 4.5 2.7 - - + -
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Residues in contact with ARG 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ASN* 3.0 47.4 + - - +
262A ALA 3.2 0.2 - - - -
263A TYR* 1.3 76.2 - - - +
265A GLY* 1.3 62.9 + - - +
267A CYS* 3.6 1.6 + - - +
268A SER* 3.1 25.6 + - - -
352A ASP* 2.4 38.7 + - - +
353A ILE* 3.6 32.3 - - + +
356A LYS* 3.7 40.8 - - + +
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Residues in contact with GLY 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ASP* 4.9 4.5 - - - -
262A ALA 4.1 5.0 + - - -
263A TYR 3.3 0.6 - - - -
264A ARG* 1.3 76.3 - - - +
266A TYR* 1.3 65.4 + - - +
268A SER* 2.9 20.9 + - - -
269A ASN* 3.2 13.0 + - - +
356A LYS* 5.6 3.1 - - - -
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Residues in contact with TYR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE 4.3 7.4 + - - -
219A PHE 3.3 28.3 - - - -
220A GLY* 4.9 1.6 - - - -
221A ASP* 3.2 31.4 + - - +
222A LEU* 3.4 19.7 - - + +
262A ALA 4.9 0.2 + - - -
263A TYR* 3.3 18.5 + + + +
265A GLY* 1.3 75.0 - - - +
267A CYS* 1.3 68.9 + - - +
269A ASN* 3.2 7.7 + - + +
270A GLN* 3.2 34.4 + - + +
308A LEU* 2.5 49.7 + - - +
311A PRO* 3.7 28.7 - - + -
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Residues in contact with CYS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A TYR* 3.0 23.8 + - - +
264A ARG 4.1 1.1 - - - +
266A TYR* 1.3 84.7 - - - +
268A SER* 1.3 61.6 + - - +
270A GLN* 3.4 24.3 + - - +
271A LEU 4.7 0.9 + - - -
311A PRO* 4.7 0.7 - - - -
312A ARG* 4.3 23.8 - - + -
315A LEU* 3.9 26.9 - - - -
353A ILE* 3.9 20.6 - - + -
357A LYS* 3.7 15.2 - - + +
69B LEU* 4.9 7.0 - - + -
72B LEU* 4.7 2.3 - - + +
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ARG 3.1 16.2 + - - -
265A GLY* 2.9 19.4 + - - -
267A CYS* 1.3 77.3 - - - +
269A ASN* 1.3 59.1 + - - +
270A GLN 3.4 0.2 - - - -
271A LEU* 4.7 7.7 + - - +
272A ALA* 5.3 0.9 + - - +
356A LYS* 4.0 21.4 + - - -
357A LYS* 4.1 14.8 - - - +
360A SER* 3.2 40.0 + - - -
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Residues in contact with ASN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A HIS* 3.0 49.0 + - - +
265A GLY 3.2 14.8 + - - +
266A TYR* 3.2 7.2 + - + +
268A SER* 1.3 77.3 - - - +
270A GLN* 1.3 65.5 + - - +
271A LEU 3.2 2.9 - - - -
272A ALA* 3.1 12.1 + - - +
273A ALA* 2.9 20.7 + - - +
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Residues in contact with GLN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A TYR* 3.2 21.8 + - + +
267A CYS* 3.5 21.9 - - - +
268A SER 3.4 1.6 - - - -
269A ASN* 1.3 77.3 - - - +
271A LEU* 1.3 57.3 + - - +
273A ALA* 3.2 9.1 + - + +
274A LYS* 2.9 29.8 + - - +
305A TRP* 3.5 34.4 - - + -
308A LEU* 3.9 11.8 + - + +
309A ASP* 2.7 39.6 + - - +
312A ARG* 3.9 14.7 - - - +
72B LEU* 3.8 20.6 - - + +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A CYS 4.7 1.6 + - - +
268A SER 4.7 6.9 + - - +
269A ASN 3.2 0.4 - - - -
270A GLN* 1.3 79.5 - - - +
272A ALA* 1.3 61.7 + - - +
274A LYS* 3.3 9.4 + - + +
275A ALA* 3.1 20.0 + - + +
357A LYS* 4.8 12.1 - - + +
361A GLU* 4.6 28.5 - - + +
364A TYR* 4.1 37.0 - - + +
365A TYR* 4.6 10.5 - - - +
72B LEU* 4.2 24.0 - - + +
75B PRO* 6.5 1.1 - - + -
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A HIS* 3.6 31.7 + - + +
268A SER 5.3 0.8 + - - +
269A ASN* 3.1 18.3 + - - +
271A LEU* 1.3 76.8 - - - +
273A ALA* 1.3 65.1 + - - +
275A ALA* 3.3 5.1 + - - +
276A LEU* 3.1 17.2 + - - +
364A TYR* 4.2 28.2 - - + -
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A HIS* 3.9 13.4 + - - +
218A ILE* 3.7 37.3 - - + +
266A TYR* 6.4 0.7 - - + -
269A ASN* 2.9 13.0 + - - +
270A GLN* 3.2 13.0 + - + +
272A ALA* 1.3 78.3 - - - +
274A LYS* 1.3 60.5 + - - +
276A LEU* 3.3 3.6 + - - +
277A LEU* 3.1 27.8 + - - +
305A TRP* 5.1 4.7 - - + -
308A LEU* 5.3 1.8 - - + -
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A GLN 2.9 15.2 + - - +
271A LEU* 3.6 12.1 - - + +
272A ALA 3.3 0.2 - - - -
273A ALA* 1.3 73.1 - - - +
275A ALA* 1.3 59.9 + - - +
277A LEU* 3.3 9.7 + - + -
278A ASP* 2.9 59.3 + - - +
305A TRP* 3.5 59.5 - - + +
72B LEU* 5.8 1.3 - - + -
75B PRO* 3.3 27.0 + - + +
76B ASP* 3.0 28.3 + - - -
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Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 3.1 13.4 + - + +
272A ALA 3.4 9.9 - - - +
273A ALA 3.2 0.2 - - - -
274A LYS* 1.3 77.1 - - - +
276A LEU* 1.3 56.6 + - - +
278A ASP* 3.4 8.6 + - - +
279A GLN* 3.0 28.2 + - - +
364A TYR* 3.5 25.1 - - + +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A GLU* 3.7 45.1 - - + +
217A HIS* 3.8 20.9 - - + +
218A ILE* 3.8 16.8 - - + -
272A ALA 3.1 12.2 + - - +
273A ALA 3.7 7.0 - - - +
274A LYS 3.3 0.2 - - - -
275A ALA* 1.3 76.5 - - - +
277A LEU* 1.3 63.6 + - - +
279A GLN* 3.1 35.5 + - - +
280A LYS* 3.0 38.6 + - + +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A MET* 4.7 8.5 - - + -
218A ILE* 3.8 23.1 - - + -
273A ALA 3.1 16.1 + - - +
274A LYS* 3.6 14.6 - - + +
276A LEU* 1.3 77.2 - - - +
278A ASP* 1.3 59.6 + - - +
280A LYS* 2.9 26.5 + - + +
281A LYS* 3.4 9.6 + - - +
286A VAL* 5.6 2.0 - - + -
287A GLN* 4.7 1.4 - - - +
290A LEU* 5.3 10.3 - - + -
304A LEU* 4.0 23.3 - - + -
305A TRP* 4.3 18.6 - - + +
308A LEU* 3.6 30.7 - - + -
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Residues in contact with ASP 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LYS* 2.9 51.5 + - - +
275A ALA* 3.7 7.3 - - - +
277A LEU* 1.3 76.5 - - - +
279A GLN* 1.3 62.0 + - - +
281A LYS* 3.2 45.0 + - + +
282A GLN 4.7 0.2 + - - -
75B PRO* 5.6 2.3 - - - +
76B ASP* 4.5 3.6 - - - +
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Residues in contact with GLN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A GLU* 5.4 1.6 + - - -
275A ALA 3.0 13.4 + - - +
276A LEU* 3.2 35.2 - - - +
278A ASP* 1.3 77.5 - - - +
280A LYS* 1.3 67.3 + - + +
281A LYS 3.2 3.0 + - - -
282A GLN* 3.7 22.6 + - - +
420A GLU* 4.7 21.6 - - + +
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Residues in contact with LYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ILE 5.4 1.4 + - - -
210A MET* 4.0 20.9 - - - +
214A GLU* 2.7 41.7 + - - -
276A LEU* 3.0 28.8 + - + +
277A LEU* 2.9 15.2 + - + +
279A GLN* 1.3 83.7 - - + +
281A LYS* 1.3 62.9 + - - +
282A GLN 3.1 2.2 - - - -
283A ASP* 3.1 34.5 + - + +
286A VAL* 3.9 29.4 - - + +
287A GLN* 2.9 14.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il